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C++ BaseMolecule::possibleBondOrder方法代码示例

本文整理汇总了C++中BaseMolecule::possibleBondOrder方法的典型用法代码示例。如果您正苦于以下问题:C++ BaseMolecule::possibleBondOrder方法的具体用法?C++ BaseMolecule::possibleBondOrder怎么用?C++ BaseMolecule::possibleBondOrder使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在BaseMolecule的用法示例。


在下文中一共展示了BaseMolecule::possibleBondOrder方法的2个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: matchQueryBond

bool MoleculeSubstructureMatcher::matchQueryBond (QueryMolecule::Bond *query,
             BaseMolecule &target, int sub_idx, int super_idx, AromaticityMatcher *am, dword flags)
{
   int i;

   // MR TODO: match topology. Query bond in ring cannot match 
   // target bond that is not in ring. But R-groups should be 
   // handled carefully

   switch (query->type)
   {
      case QueryMolecule::OP_NONE:
         return true;
      case QueryMolecule::OP_AND:
         for (i = 0; i < query->children.size(); i++)
            if (!matchQueryBond(query->child(i), target, sub_idx, super_idx, am, flags))
               return false;
         return true;
      case QueryMolecule::OP_OR:
         for (i = 0; i < query->children.size(); i++)
            if (matchQueryBond(query->child(i), target, sub_idx, super_idx, am, flags))
               return true;
         return false;
      case QueryMolecule::OP_NOT:
         return !matchQueryBond(query->child(0), target, sub_idx, super_idx, am, 
            flags ^ MATCH_DISABLED_AS_TRUE);

      case QueryMolecule::BOND_ORDER:
      {
         if (flags & MATCH_BOND_TYPE)
         {
            if (am != 0)
            {
               if (target.getBondOrder(super_idx) == BOND_AROMATIC)
                  return am->canFixQueryBond(sub_idx, true);
               else 
               {
                  if (!am->canFixQueryBond(sub_idx, false))
                     return false;
               }
            }
            return target.possibleBondOrder(super_idx, query->value);
         }
         return (flags & MATCH_DISABLED_AS_TRUE) != 0;
      }
      case QueryMolecule::BOND_TOPOLOGY:
         return target.getEdgeTopology(super_idx) == query->value;
      case QueryMolecule::HIGHLIGHTING:
         return query->value == (int)target.isAtomHighlighted(super_idx);
      default:
         throw Error("bad query bond type: %d", query->type);
   }
}
开发者ID:mojca,项目名称:indigo,代码行数:53,代码来源:molecule_substructure_matcher.cpp

示例2: isGeomStereoBond

bool MoleculeCisTrans::isGeomStereoBond (BaseMolecule &mol, int bond_idx,
                                         int *substituents, bool have_xyz)
{
   int substituents_local[4];

   if (substituents == 0)
      substituents = substituents_local;

   // it must be [C,N,Si,Ge]=[C,N,Si,Ge] bond
   if (!mol.possibleBondOrder(bond_idx, BOND_DOUBLE))
      return false;

   const Edge &edge = mol.getEdge(bond_idx);
   int beg_idx = edge.beg;
   int end_idx = edge.end;

   if (!mol.possibleAtomNumber(beg_idx, ELEM_C) &&
       !mol.possibleAtomNumber(beg_idx, ELEM_N) &&
       !mol.possibleAtomNumber(beg_idx, ELEM_Si) &&
       !mol.possibleAtomNumber(beg_idx, ELEM_Ge))
      return false;
   if (!mol.possibleAtomNumber(end_idx, ELEM_C) &&
       !mol.possibleAtomNumber(end_idx, ELEM_N) &&
       !mol.possibleAtomNumber(end_idx, ELEM_Si) &&
       !mol.possibleAtomNumber(end_idx, ELEM_Ge))
      return false;

   // Double bonds with R-sites are excluded because cis-trans configuration 
   // cannot be determined when R-site is substituted with R-group
   if (mol.isRSite(beg_idx) || mol.isRSite(end_idx))
      return false;

   // the atoms should have 1 or 2 single bonds
   // (apart from the double bond under consideration)
   const Vertex &beg = mol.getVertex(beg_idx);
   const Vertex &end = mol.getVertex(end_idx);

   if (beg.degree() < 2 || beg.degree() > 3 ||
       end.degree() < 2 || end.degree() > 3)
      return false;

   substituents[0] = -1;
   substituents[1] = -1;
   substituents[2] = -1;
   substituents[3] = -1;

   int i;

   for (i = beg.neiBegin(); i != beg.neiEnd(); i = beg.neiNext(i))
   {
      int nei_edge_idx = beg.neiEdge(i);

      if (nei_edge_idx == bond_idx)
         continue;
      
      if (!mol.possibleBondOrder(nei_edge_idx, BOND_SINGLE))
         return false;

      if (substituents[0] == -1)
         substituents[0] = beg.neiVertex(i);
      else // (substituents[1] == -1)
         substituents[1] = beg.neiVertex(i);
   }

   for (i = end.neiBegin(); i != end.neiEnd(); i = end.neiNext(i))
   {
      int nei_edge_idx = end.neiEdge(i);

      if (nei_edge_idx == bond_idx)
         continue;
      
      if (!mol.possibleBondOrder(nei_edge_idx, BOND_SINGLE))
         return false;

      if (substituents[2] == -1)
         substituents[2] = end.neiVertex(i);
      else // (substituents[3] == -1)
         substituents[3] = end.neiVertex(i);
   }

   // Check trianges when substituents are the same: CC1=C(N)C1
   if (substituents[0] >= 0)
      if (substituents[0] == substituents[2] || substituents[0] == substituents[3])
         return false;
   if (substituents[1] >= 0)
      if (substituents[1] == substituents[2] || substituents[1] == substituents[3])
         return false;

   if (have_xyz)
   {
      if (substituents[1] != -1 &&
          _sameside(mol, beg_idx, end_idx, substituents[0], substituents[1]) != -1)
         return false;
      else if (_sameline(mol, beg_idx, end_idx, substituents[0]))
         return false;

      if (substituents[3] != -1 &&
          _sameside(mol, beg_idx, end_idx, substituents[2], substituents[3]) != -1)
         return false;
      else if (_sameline(mol, beg_idx, end_idx, substituents[2]))
//.........这里部分代码省略.........
开发者ID:mojca,项目名称:indigo,代码行数:101,代码来源:molecule_cis_trans.cpp


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